David Henderson
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/GeneticsPed |
| git_branch: devel |
| git_last_commit: 6d4c66d |
| git_last_commit_date: 2025-04-15 09:40:14 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:03 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 832/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneticsPed 1.71.0 (landing page) David Henderson
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
To the developers/maintainers of the GeneticsPed package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneticsPed.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: GeneticsPed |
| Version: 1.71.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GeneticsPed |
| StartedAt: 2025-10-23 15:05:06 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 15:05:24 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 18.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GeneticsPed
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GeneticsPed’ ...
** this is package ‘GeneticsPed’ version ‘1.71.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ainverse.cc -o ainverse.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c eibd.cc -o eibd.o
gfortran -fpic -g -O2 -Wall -Werror=format-security -c ggmatmult.f -o ggmatmult.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
gfortran -fpic -g -O2 -Wall -Werror=format-security -c gpi.f -o gpi.o
f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c inbreed.cc -o inbreed.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c inverseAdditive.cc -o inverseAdditive.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c meuwissen.cc -o meuwissen.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c pedSort.cc -o pedSort.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c pedtemplate.cc -o pedtemplate.o
pedtemplate.cc: In member function ‘void Pedigree::ShowPed()’:
pedtemplate.cc:373:15: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘__gnu_cxx::__normal_iterator<TPed*, std::vector<TPed> >::difference_type’ {aka ‘long int’} [-Wformat=]
373 | Rprintf("%d\t", p - pedigree.begin());
| ~^ ~~~~~~~~~~~~~~~~~~~~
| | |
| int __gnu_cxx::__normal_iterator<TPed*, std::vector<TPed> >::difference_type {aka long int}
| %ld
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c register.cc -o register.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c sargolzaei.c -o sargolzaei.o
sargolzaei.c: In function ‘sargolzaei’:
sargolzaei.c:52:32: warning: ‘*Ped[S][0]’ may be used uninitialized [-Wmaybe-uninitialized]
52 | rPed[rN][0] = Link[Ped[S][0]];
| ~~~~~~^~~
sargolzaei.c:53:34: warning: ‘*Ped[D][1]’ may be used uninitialized [-Wmaybe-uninitialized]
53 | rPed[rN++][1] = Link[Ped[D][1]];
| ~~~~~~^~~
sargolzaei.c:58:32: warning: ‘*Ped[D][0]’ may be used uninitialized [-Wmaybe-uninitialized]
58 | rPed[rN][0] = Link[Ped[D][0]];
| ~~~~~~^~~
sargolzaei.c:59:34: warning: ‘*Ped[D][1]’ may be used uninitialized [-Wmaybe-uninitialized]
59 | rPed[rN++][1] = Link[Ped[D][1]];
| ~~~~~~^~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c sortped.cc -o sortped.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o GeneticsPed.so ainverse.o eibd.o ggmatmult.o gpi.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sargolzaei.o sortped.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-GeneticsPed/00new/GeneticsPed/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GeneticsPed)